R: Inverse Relatedness Matrix and Phylogenetic Covariance Matrix

inverseA {MCMCglmm} | R Documentation

## Inverse Relatedness Matrix and Phylogenetic Covariance Matrix

### Description

Henderson (1976) and Meuwissen and Luo (1992) algorithm for inverting relatedness matrices, and Hadfield and Nakagawa (2010) algorithm for inverting phylogenetic covariance matrices.

### Usage

      inverseA(pedigree=NULL, nodes="ALL", scale=TRUE, reduced=FALSE,
         tol = .Machine$double.eps^0.5)

### Arguments

`pedigree` | ordered pedigree with 3 columns: id, dam and sire, or a `phylo` object.
`nodes` | `"ALL"` calculates the inverse for all individuals/nodes. For phylogenies `"TIPS"` calculates the inverse for the species tips only, and for pedigrees a vector of id's can be passed which inverts the relatedness matrix for that subset.
`scale` | logical: should a phylogeny (needs to be ultrametric) be scaled to unit length (distance from root to tip)?
`reduced` | logical: should childless nodes be dropped from the inverse and the pedigree/phylogeny representation be reduced?
`tol` | numeric: differences in branch length smaller than this are ignored when assessing whether a tree is ultrametric.

### Value

`Ainv` | inverse as `sparseMatrix`
`inbreeding` | inbreeding coefficients/branch lengths
`pedigree` | pedigree/pedigree representation of phylogeny

### Author(s)

Jarrod Hadfield j.hadfield@ed.ac.uk

### References

Henderson, C.R. (1976) Biometrics 32 (1) 69:83

Quaas, R. L. and Pollak, E. J. (1980) Journal of Animal Science 51:1277-1287.

Meuwissen, T.H.E and Luo, Z. (1992) Genetic Selection Evolution 24 (4) 305:313

Hadfield, J.D. and Nakagawa, S. (2010) Journal of Evolutionary Biology 23 494-508

### Examples

    data(bird.families)
    Ainv<-inverseA(bird.families)

[Package MCMCglmm version 2.30 Index]